So I'm back poking at this.
After some careful measurement and a bit of poking on digikey, I managed to actually figure out what the connector model number for the "FAN_SIG_CONN" connector on the motherboard is. I picked up connectors for both interfaces:
View attachment 10157
At that point, the challenge was figuring out what the connections actually do. Poking with an oscilloscope and DMM yielded 8 apparent PWM outputs, 8 pins sitting at ~10.8V, and 4 grounds.
Since I assume there isn't a external controller that runs the fan, my guess was that the 8 mostly-high pins were supposed to be connected to the open-collector tachometer output on your common 4-wire computer fan. As such, I set up a signal generator to generate a fake ran signal, put a 2.2KΩ resistor in series so I wouldn't blow up anything if I were wrong (hopefully), and stuck that on the probable fan inputs:
View attachment 10158
And Bam: IPMI is reporting the fan is no longer missing!
(This was supposed to be a screenshot of the IPMI interface, but apparently I can't hold two oscilloscope probes AND take a picture with my cell-phone at the same time)
View attachment 10156
Anyways, the IPMI interface is reporting the fan running at 1200 RPM, and I can change the fan speed by adjusting the signal generator.
I also finally made a proper drawing of the hole locations:
View attachment 10160